Spatial outbreak detection analysis tool : a system to create sets of semi-synthetic geo-spatial clusters

Thesis (M. Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (leaves 55-57).Syndromic surveillance systems, especially software systems, have emerged as the leading outbreak detection mechanisms. Early outbreak detection systems can assist with medical and logistic decision support. One important concern for effectively testing these systems in practice is the scarcity of authentic outbreak health data. Because of this shortage, creating suitable geotemporal test clusters for surveillance algorithm validation is essential. Described is an automated tool that creates artificial patient clusters by varying a large variety of realistic outbreak parameters. The cluster creation tool is an open-source program that accepts a set of outbreak parameters and creates artificial geospatial patient data for a single cluster or a series of similar clusters. This helps automate the process of rigorous testing and validation of outbreak detection algorithms. Using the cluster generator, single patient clusters and series of patient clusters were created - as files and series of files containing patient longitude and latitude coordinates. These clusters were then tested and validated using a publicly-available GIS visualization program. All generated clusters were properly created within the ranges that were entered as parameters at program execution. Sample semi-synthetic datasets from the cluster creation tool were then used to validate a popular spatial outbreak detection algorithm, the M-Statistic.by Christopher A. Casa.M.Eng.and S.B

An unsupervised classification method for inferring original case locations from low-resolution disease maps

BACKGROUND: Widespread availability of geographic information systems software has facilitated the use of disease mapping in academia, government and private sector. Maps that display the address of affected patients are often exchanged in public forums, and published in peer-reviewed journal articles. As previously reported, a search of figure legends in five major medical journals found 19 articles from 1994–2004 that identify over 19,000 patient addresses. In this report, a method is presented to evaluate whether patient privacy is being breached in the publication of low-resolution disease maps. RESULTS: To demonstrate the effect, a hypothetical low-resolution map of geocoded patient addresses was created and the accuracy with which patient addresses can be resolved is described. Through georeferencing and unsupervised classification of the original image, the method precisely re-identified 26% (144/550) of the patient addresses from a presentation quality map and 79% (432/550) from a publication quality map. For the presentation quality map, 99.8% of the addresses were within 70 meters (approximately one city block length) of the predicted patient location, 51.6% of addresses were identified within five buildings, 70.7% within ten buildings and 93% within twenty buildings. For the publication quality map, all addresses were within 14 meters and 11 buildings of the predicted patient location. CONCLUSION: This study demonstrates that lowering the resolution of a map displaying geocoded patient addresses does not sufficiently protect patient addresses from re-identification. Guidelines to protect patient privacy, including those of medical journals, should reflect policies that ensure privacy protection when spatial data are displayed or published

Online information on medical cannabis is not always aligned with scientific evidence and may raise unrealistic expectations

There is a growing literature on the potential medical uses of Cannabis sativa and cannabinoid compounds. Although these have only been approved by regulatory agencies for a few indications, there is a hype about their possible benefits in a variety of conditions and a large market in the wellness industry. As in many cases patients search for information on cannabis products online, we have analyzed the information on medical cannabis available on the Internet. Therefore, this study aims at assessing the quality of the information available online on medical cannabis

Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations

Summary: Accurate annotations of genomic variants are necessary to achieve full-genome clinical interpretations that are scientifically sound and medically relevant. Many disease associations, especially those reported before the completion of the HGP, are limited in applicability because of potential inconsistencies with our current standards for genomic coordinates, nomenclature and gene structure. In an effort to validate and link variants from the medical genetics literature to an unambiguous reference for each variant, we developed a software pipeline and reviewed 68 641 single amino acid mutations from Online Mendelian Inheritance in Man (OMIM), Human Gene Mutation Database (HGMD) and dbSNP. The frequency of unresolved mutation annotations varied widely among the databases, ranging from 4 to 23%. A taxonomy of primary causes for unresolved mutations was produced

Experimental study exploring the interaction of structural and leakage dynamics

Strategies for managing leakage from water distribution systems require the ability to effectively evaluate such real losses through the understanding of the behavior of individual leaks, including their response to changes in pressure regime due to demand or management strategies. This paper presents the results from an innovative experimental investigation aimed at understanding the response of longitudinal slits in pressurized viscoelastic pipes, specifically considering the interaction between the structural and leakage dynamics. For the first time, leakage flow rate, pressure, leak area, and material strain were recorded simultaneously, providing new knowledge of the complex interaction of these factors. The paper shows that strain and area are directly related, hence it is possible to employ strain as a predictor of leak area, calculated using a calibrated viscoelastic model. Using such an approach, the leakage flow rates under a range of quasi-static pressures were accurately predicted and validated. Overall the paper demonstrates that the orifice equation, with a constant coefficient of discharge, is suitable for accurately estimating dynamic leakage flow rates from longitudinal slits, provided that the leak area is suitably incorporated

An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs

Indivo: a personally controlled health record for health information exchange and communication

<p>Abstract</p> <p>Background</p> <p>Personally controlled health records (PCHRs), a subset of personal health records (PHRs), enable a patient to assemble, maintain and manage a secure copy of his or her medical data. Indivo (formerly PING) is an open source, open standards PCHR with an open application programming interface (API).</p> <p>Results</p> <p>We describe how the PCHR platform can provide standard building blocks for networked PHR applications. Indivo allows the ready integration of diverse sources of medical data under a patient's control through the use of standards-based communication protocols and APIs for connecting PCHRs to existing and future health information systems.</p> <p>Conclusion</p> <p>The strict and transparent personal control model is designed to encourage widespread participation by patients, healthcare providers and institutions, thus creating the ecosystem for development of innovative, consumer-focused healthcare applications.</p

Using GIS to create synthetic disease outbreaks

BACKGROUND: The ability to detect disease outbreaks in their early stages is a key component of efficient disease control and prevention. With the increased availability of electronic health-care data and spatio-temporal analysis techniques, there is great potential to develop algorithms to enable more effective disease surveillance. However, to ensure that the algorithms are effective they need to be evaluated. The objective of this research was to develop a transparent user-friendly method to simulate spatial-temporal disease outbreak data for outbreak detection algorithm evaluation. A state-transition model which simulates disease outbreaks in daily time steps using specified disease-specific parameters was developed to model the spread of infectious diseases transmitted by person-to-person contact. The software was developed using the MapBasic programming language for the MapInfo Professional geographic information system environment. RESULTS: The simulation model developed is a generalised and flexible model which utilises the underlying distribution of the population and incorporates patterns of disease spread that can be customised to represent a range of infectious diseases and geographic locations. This model provides a means to explore the ability of outbreak detection algorithms to detect a variety of events across a large number of stochastic replications where the influence of uncertainty can be controlled. The software also allows historical data which is free from known outbreaks to be combined with simulated outbreak data to produce files for algorithm performance assessment. CONCLUSION: This simulation model provides a flexible method to generate data which may be useful for the evaluation and comparison of outbreak detection algorithm performance

Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation

Background and aims: Very early onset inflammatory bowel disease [VEOIBD] is characterized by intestinal inflammation affecting infants and children less than 6 years of age. To date, over 60 monogenic aetiologies of VEOIBD have been identified, many characterized by highly penetrant recessive or dominant variants in underlying immune and/or epithelial pathways. We sought to identify the genetic cause of VEOIBD in a subset of patients with a unique clinical presentation. Methods: Whole exome sequencing was performed on five families with ten patients who presented with a similar constellation of symptoms including medically refractory infantile-onset IBD, bilateral sensorineural hearing loss and, in the majority, recurrent infections. Genetic aetiologies of VEOIBD were assessed and Sanger sequencing was performed to confirm novel genetic findings. Western analysis on peripheral blood mononuclear cells and functional studies with epithelial cell lines were employed. Results: In each of the ten patients, we identified damaging heterozygous or biallelic variants in the Syntaxin-Binding Protein 3 gene [STXBP3], a protein known to regulate intracellular vesicular trafficking in the syntaxin-binding protein family of molecules, but not associated to date with either VEOIBD or sensorineural hearing loss. These mutations interfere with either intron splicing or protein stability and lead to reduced STXBP3 protein expression. Knock-down of STXBP3 in CaCo2 cells resulted in defects in cell polarity. Conclusion: Overall, we describe a novel genetic syndrome and identify a critical role for STXBP3 in VEOIBD, sensorineural hearing loss and immune dysregulation.info:eu-repo/semantics/publishedVersio